PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
4FEG
Biol. Unit 1
Info
Asym.Unit (490 KB)
Biol.Unit 1 (959 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HIGH-RESOLUTION STRUCTURE OF PYRUVATE OXIDASE IN COMPLEX WITH REACTION INTERMEDIATE 2-HYDROXYETHYL-THIAMIN DIPHOSPHATE CARBANION-ENAMINE, CRYSTAL A
Authors
:
D. Meyer, P. Neumann, E. Koers, H. Sjuts, S. Luedtke, G. M. Sheldrick, R. K. Tittmann
Date
:
30 May 12 (Deposition) - 20 Jun 12 (Release) - 25 Jul 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.09
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Carbanion, Structure Activity Relationship, Oxidation-Reduction, Umpolung, Thiamine Diphosphate, Reaction Intermediate, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Meyer, P. Neumann, E. Koers, H. Sjuts, S. Ludtke, G. M. Sheldrick, R. Ficner, K. Tittmann
Unexpected Tautomeric Equilibria Of The Carbanion-Enamine Intermediate In Pyruvate Oxidase Highlight Unrecognized Chemical Versatility Of Thiamin.
Proc. Natl. Acad. Sci. Usa V. 109 10867 2012
[
close entry info
]
Hetero Components
(5, 36)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
5a: PYRUVIC ACID (PYRa)
5b: PYRUVIC ACID (PYRb)
5c: PYRUVIC ACID (PYRc)
5d: PYRUVIC ACID (PYRd)
6a: 2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMI... (TDMa)
6b: 2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMI... (TDMb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
GOL
16
Ligand/Ion
GLYCEROL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
PO4
4
Ligand/Ion
PHOSPHATE ION
5
PYR
8
Ligand/Ion
PYRUVIC ACID
6
TDM
4
Ligand/Ion
2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE
[
close Hetero Component info
]
Sites
(20, 20)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:555 , ARG A:556 , LEU A:557 , ASP A:558 , MET A:561 , SER A:562 , HOH A:977 , HOH A:1633 , HOH A:1687
BINDING SITE FOR RESIDUE PYR A 701
02
AC2
SOFTWARE
PHE A:121 , ASN A:263 , ARG A:264 , FAD A:709 , HOH A:1258 , HOH A:1488
BINDING SITE FOR RESIDUE PYR A 702
03
AC3
SOFTWARE
GLY A:34 , GLY A:35 , SER A:36 , SER A:82 , PHE A:111 , GLN A:122 , ILE A:480 , TDM A:708 , HOH A:909 , HOH A:956 , HOH A:1679 , HOH A:1766
BINDING SITE FOR RESIDUE PO4 A 703
04
AC4
SOFTWARE
TRP A:24 , LYS A:75 , TYR A:158 , TYR A:189 , HOH A:1032 , HOH A:1684 , HOH B:7778
BINDING SITE FOR RESIDUE GOL A 704
05
AC5
SOFTWARE
LYS A:433 , PRO A:437 , GLU A:438 , PRO A:466 , ALA A:533 , GLN A:534 , HOH A:1047 , HOH A:1225 , HOH A:1483
BINDING SITE FOR RESIDUE GOL A 705
06
AC6
SOFTWARE
ARG A:156 , HIS A:160 , HOH A:849 , HOH A:894 , HOH A:1701 , ASN B:286 , LYS B:311 , LYS B:314 , HOH B:7143
BINDING SITE FOR RESIDUE GOL A 706
07
AC7
SOFTWARE
ASP A:447 , ASN A:474 , GLN A:476 , TDM A:708 , HOH A:1632
BINDING SITE FOR RESIDUE MG A 707
08
AC8
SOFTWARE
PRO A:33 , GLU A:59 , SER A:82 , PRO A:85 , HIS A:89 , GLN A:122 , VAL A:394 , ASP A:396 , ALA A:420 , MET A:422 , GLY A:446 , ASP A:447 , GLY A:448 , GLY A:449 , ASN A:474 , GLN A:476 , TYR A:477 , GLY A:478 , PHE A:479 , ILE A:480 , PO4 A:703 , MG A:707 , FAD A:709 , HOH A:813 , HOH A:822 , HOH A:847 , HOH A:1632
BINDING SITE FOR RESIDUE TDM A 708
09
AC9
SOFTWARE
HIS A:101 , PHE A:121 , GLY A:220 , ILE A:221 , GLY A:222 , THR A:244 , TYR A:245 , ALA A:262 , ASN A:263 , ARG A:264 , VAL A:265 , GLY A:284 , ASN A:285 , ASN A:286 , PRO A:288 , PHE A:289 , ASP A:306 , ILE A:307 , ASP A:308 , LYS A:311 , ALA A:324 , ASP A:325 , ALA A:326 , ASN A:398 , SER A:416 , ASN A:417 , PYR A:702 , TDM A:708 , HOH A:802 , HOH A:805 , HOH A:806 , HOH A:835 , HOH A:1350 , HOH A:1423 , HOH A:1642
BINDING SITE FOR RESIDUE FAD A 709
10
BC1
SOFTWARE
TRP A:174 , THR A:487 , GLN A:489 , HOH A:978 , HOH A:1268 , HOH A:1630
BINDING SITE FOR RESIDUE GOL A 710
11
BC2
SOFTWARE
LEU B:555 , ARG B:556 , LEU B:557 , ASP B:558 , MET B:561 , SER B:562 , HOH B:7219 , HOH B:7320 , HOH B:7670
BINDING SITE FOR RESIDUE PYR B 701
12
BC3
SOFTWARE
PHE B:121 , ASN B:263 , ARG B:264 , FAD B:710 , HOH B:7316 , HOH B:7680
BINDING SITE FOR RESIDUE PYR B 702
13
BC4
SOFTWARE
GLY B:34 , GLY B:35 , SER B:36 , SER B:82 , PHE B:111 , GLN B:122 , ILE B:480 , TDM B:709 , HOH B:7057 , HOH B:7131 , HOH B:7828
BINDING SITE FOR RESIDUE PO4 B 703
14
BC5
SOFTWARE
GLY B:25 , ASP B:27 , HIS B:28 , ASP B:69 , THR B:73 , LYS B:75 , ILE B:76 , ASN B:435 , HOH B:7034 , HOH B:7615 , HOH B:7802 , HOH B:7835
BINDING SITE FOR RESIDUE GOL B 704
15
BC6
SOFTWARE
HOH A:1012 , ALA B:569 , PHE B:570 , ARG B:573 , TYR B:574 , HOH B:7137 , HOH B:7144 , HOH B:7887
BINDING SITE FOR RESIDUE GOL B 705
16
BC7
SOFTWARE
LYS B:433 , PRO B:437 , GLU B:438 , PRO B:466 , ALA B:533 , GLN B:534 , HOH B:7346 , HOH B:7638
BINDING SITE FOR RESIDUE GOL B 706
17
BC8
SOFTWARE
PRO B:409 , ARG B:412 , HOH B:7114 , HOH B:7178 , HOH B:7395 , HOH B:7575 , HOH B:7792
BINDING SITE FOR RESIDUE GOL B 707
18
BC9
SOFTWARE
ASP B:447 , ASN B:474 , GLN B:476 , TDM B:709 , HOH B:7798
BINDING SITE FOR RESIDUE MG B 708
19
CC1
SOFTWARE
PRO B:33 , GLU B:59 , SER B:82 , PRO B:85 , HIS B:89 , GLN B:122 , VAL B:394 , ASP B:396 , ALA B:420 , MET B:422 , GLY B:446 , ASP B:447 , GLY B:448 , GLY B:449 , ASN B:474 , GLN B:476 , TYR B:477 , GLY B:478 , PHE B:479 , ILE B:480 , PO4 B:703 , MG B:708 , FAD B:710 , HOH B:7010 , HOH B:7023 , HOH B:7045 , HOH B:7798
BINDING SITE FOR RESIDUE TDM B 709
20
CC2
SOFTWARE
HIS B:101 , PHE B:121 , GLY B:220 , ILE B:221 , GLY B:222 , THR B:244 , TYR B:245 , PRO B:246 , ALA B:262 , ASN B:263 , ARG B:264 , VAL B:265 , GLY B:284 , ASN B:285 , ASN B:286 , TYR B:287 , PRO B:288 , PHE B:289 , ASP B:306 , ILE B:307 , ASP B:308 , LYS B:311 , ALA B:324 , ASP B:325 , ALA B:326 , ASN B:398 , SER B:416 , ASN B:417 , PYR B:702 , TDM B:709 , HOH B:7001 , HOH B:7003 , HOH B:7015 , HOH B:7019 , HOH B:7611 , HOH B:7675 , HOH B:7739
BINDING SITE FOR RESIDUE FAD B 710
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d4fega2 (A:183-365)
1b: SCOP_d4fegb2 (B:183-365)
2a: SCOP_d4fega1 (A:9-182)
2b: SCOP_d4fega3 (A:366-591)
2c: SCOP_d4fegb1 (B:9-182)
2d: SCOP_d4fegb3 (B:366-591)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
DHS-like NAD/FAD-binding domain
(176)
Superfamily
:
DHS-like NAD/FAD-binding domain
(176)
Family
:
automated matches
(36)
Protein domain
:
automated matches
(36)
Lactobacillus plantarum [TaxId: 644042]
(3)
1a
d4fega2
A:183-365
1b
d4fegb2
B:183-365
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
automated matches
(65)
Protein domain
:
automated matches
(65)
Lactobacillus plantarum [TaxId: 644042]
(3)
2a
d4fega1
A:9-182
2b
d4fega3
A:366-591
2c
d4fegb1
B:9-182
2d
d4fegb3
B:366-591
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
Asymmetric Unit 2
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (490 KB)
Header - Asym.Unit
Biol.Unit 1 (959 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
4FEG
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help